CEO of the Food and Grocery Council of Australia, Kate Carnell, said she could not comment on individual price hikes, but said generally, the increased cost of refundable containers did not account for refunds valid for containers bought before the scheme launched.

"Right at the moment, there is no way of telling the difference between a can or bottle or plastic that was sold before January 1 or after January 1," Mr Carnell said.

She said price increases accounted for costs and administration associated with the new scheme.

"The Government sold this system to the Territory as something that would solve littler - that means people are being encouraged to pick up bottles and cans and take them to collection deposits."

She said it would be possible that initially, collectors would receive more than a 100 per cent return of containers sold after January 1, with no way of tracking where containers would come from in the first 18 months of the scheme.

But the Consumer Affairs watchdog has warned unwarranted price hikes could result in hefty fines of up to $1.1m.

Meanwhile, Winelle collection depot manager Greg Meyer claimed he is at the mercy of the system, and will lose money if he accepts the terms of coordinators who administer the refunds.

"When people bring their cans in to us, we have to sort them each into coordinators - that's a representative of the manufacturer," Mr Meyer said.

"There are about 4000 to 5000 containers I can't do anything with because I don't have an agreement with the coordinators," he said, adding that the coordinators were offering 30 per cent less for refunds than they did in South Australia, where the scheme already exists.

Mr Meyer said of an estimated 300 million containers coming into the Territory each year, around 55-60 per cent was being recycled.

"So that's 120 million containers that will be lost that no one will get their refund back on - if you looked at it in a realistic manner, I would say most stuff would not have to go up more than about 12 or 12.5 cents for the consumer."

Consumers are encouraged to contact the Consumer Affairs Commissioner if they are suspicious of unwarranted price hikes.